'Method to see genetic activity in tissues developed'

Researchers have designed "acoustic reporter genes" that can penetrate deeply into tissues and report the genetic activity happening in cells in an ultrasound scan.

In the study, published in the journal Science, researchers used special chunks of DNA that spy on the chemical processes happening within cells and report on their functioning.

These genes enable researchers to get a sense of what cells are doing by observing which of the tissue's functions, embedded in their genes, turned on and off, the study noted.

The researchers, including those from California Institute of Technology (Caltech) in the US, said that reporter genes worked by encoding proteins that can be seen from outside the cell.

But for long, they said that scientists relied on reporter genes that caused cells to produce the brightly glowing green fluorescent protein (GFP).

For example, if a scientist wanted to learn about the process behind a cell becoming a neuron, they would insert the GFP gene alongside a neuronal gene into an embryo's DNA, the researchers said.

So when cells in the embryo turned on the neuron gene, they would also express the GFP gene, making the cell glow green, allowing researchers to see which genetic processes made the neurons form.

But, the researchers said that a big limitation in the process was that the light from such reporters would not penetrate well through most living tissue.

The new reporter gene allows researchers to see the genetic activity happening within cells using ultrasound which, they said, can penetrate deeply through tissue.

The "acoustic reporter genes," developed by the researchers, borrowed proteins from a species of buoyant bacteria that contained tiny air-filled protein compartments called gas vesicles.

Since the gas vesicles showed up strongly in ultrasound imaging, the researchers found a way to engineer cells to form these tiny structures when a specific genetic program was active -- enabling the process to be highlighted under ultrasound scans.

To achieve this, the researchers transplanted a genetic program of nine genes from a bacteria into mammalian cells -- cells derived from human kidneys (HEK cells), which the researchers said had never been done before.

The study noted that this was a complex process since bacteria and mammals read their respective genetic codes differently.

So even if the reporter gene was attached successfully to the bacterial DNA and inserted into the cells, the researchers said that they were not sure if the human kidney cells would process the DNA as expected.

"The translation machinery is very different in the two kinds of cells," said co-author of the study Arash Farhadi from the Heritage Medical Research Institute in the US.

Farhadi said that the process by which bacterial cells processed DNA and made the intermediary RNA molecules involved in protein making was different from how the mammalian cells did it.

"One of the biggest differences is that in bacteria it is common to have multiple genes arranged in the DNA such that they are transcribed into one shared piece of RNA, which is then translated into all the corresponding proteins, whereas in eukaryotes, every gene is usually on its own," Farhadi explained.

The researchers found a solution from yet another source of DNA -- viruses.

"Viruses also need to trick mammalian cells into expressing a bunch of proteins," said Mikhail Shapiro, co-author of the paper from Caltech.

The research team used DNA from viruses to trick the cell into producing multiple genes from a shared piece of RNA.

Using this approach, Shapiro and his team combined eight genes together on a single piece of RNA.

However, even with this done, the cells were making the expected proteins, but not in the right ratios for them to assemble into the gas vesicles.

"A building might be made of wood, glass, and bricks, but if workers show up with mostly windows and only a few bricks, they will not be able to construct a building," Shapiro explained.

The researchers said that it took several years of systematic experimentation to make the mammalian cells produce the right ratio of the gas vesicle proteins.

Now they hope to use the method to study gene expression in tumours, immune cells, neurons, and other cell types in living organisms.

"There has been more than 20 years of work improving fluorescent proteins, and we probably have 20 years of work to improve what we've developed, but this is a key proof of concept," Shapiro said.